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Xavier Thompson
cython
Commits
349dd60e
Commit
349dd60e
authored
Aug 22, 2011
by
Mark Florisson
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Added documentation
parent
aa896981
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3
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208 additions
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6 deletions
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-6
Cython/Utility/MemoryView.pyx
Cython/Utility/MemoryView.pyx
+6
-6
docs/src/userguide/index.rst
docs/src/userguide/index.rst
+1
-0
docs/src/userguide/memoryviews.rst
docs/src/userguide/memoryviews.rst
+201
-0
No files found.
Cython/Utility/MemoryView.pyx
View file @
349dd60e
...
...
@@ -330,8 +330,8 @@ cdef class memoryview(object):
transpose_memslice
(
&
result
.
from_slice
)
return
result
property
_obj
:
@
cname
(
'__pyx_memoryview__get__obj'
)
property
object
:
@
cname
(
'__pyx_memoryview__get__obj
ect
'
)
def
__get__
(
self
):
if
(
self
.
obj
is
None
and
<
PyObject
*>
self
.
view
.
obj
!=
NULL
and
self
.
view
.
obj
is
not
None
):
...
...
@@ -357,10 +357,10 @@ cdef class memoryview(object):
return
tuple
([
self
.
view
.
suboffsets
[
i
]
for
i
in
xrange
(
self
.
view
.
ndim
)])
def
__repr__
(
self
):
return
"<MemoryView of %r at 0x%x>"
%
(
self
.
_obj
.
__class__
.
__name__
,
id
(
self
))
return
"<MemoryView of %r at 0x%x>"
%
(
self
.
object
.
__class__
.
__name__
,
id
(
self
))
def
__str__
(
self
):
return
"<MemoryView of %r object>"
%
(
self
.
_obj
.
__class__
.
__name__
,)
return
"<MemoryView of %r object>"
%
(
self
.
object
.
__class__
.
__name__
,)
@
cname
(
'__pyx_memoryview_new'
)
...
...
@@ -689,8 +689,8 @@ cdef class _memoryviewslice(memoryview):
else
:
memoryview
.
assign_item_from_object
(
self
,
itemp
,
value
)
property
_obj
:
@
cname
(
'__pyx_memoryviewslice__get__obj'
)
property
object
:
@
cname
(
'__pyx_memoryviewslice__get__obj
ect
'
)
def
__get__
(
self
):
return
self
.
from_object
...
...
docs/src/userguide/index.rst
View file @
349dd60e
...
...
@@ -18,6 +18,7 @@ Contents:
limitations
pyrex_differences
early_binding_for_speed
memoryviews
parallelism
debugging
...
...
docs/src/userguide/memoryviews.rst
0 → 100644
View file @
349dd60e
.. highlight:: cython
.. _memoryviews:
**************************
Typed Memoryviews
**************************
Typed memoryviews can be used for efficient access to buffers. It is similar to the
current buffer support, but has more features and cleaner syntax. A memoryview
can be used in any context (function parameters, module-level, cdef class attribute, etc)
and can be obtained from any object that exposes the PEP 3118 buffer interface.
Memoryview slices
====================
Copying
--------
Memoryview slices can be obtained as follows::
cdef int[:, :] myslice = obj
The memoryview slice can then be efficiently indexed and sliced in GIL and nogil mode.
In GIL mode these slices can also be transposed (which gives a new memoryview slice), or
copied to a C or Fortran contiguous array::
# This slice is C contiguous
cdef int[:, ::1] c_contiguous_slice = myslice.copy()
# This slice is Fortran contiguous
cdef int[::1, :] f_contiguous_slice = myslice.copy_fortran()
print c_contiguous_slice.is_c_contig()
print f_contiguous_slice.is_f_contig()
The `::1` in the slice type specification indicates in which dimension the data is contiguous.
It can only be used to specify full C or Fortran contiguity.
Indexing and Slicing
--------------------
Indexing and slicing can be done with or without the GIL. It basically works like numpy. If
indices are specified for every dimension you will get specify an element of the base type
(e.g. `int`), otherwise you will get a new view. An Ellipsis means you get consecutive slices
for every unspecified dimension::
cdef int[:, :, :] slice = ...
# These are all equivalent
slice[10]
slice[10, :, :]
slice[10, ...]
Transposing
-----------
If all dimensions are direct (i.e., there are no indirections through pointers), then
the slice can be transposed in the same way that numpy slices can be transposed::
cdef int[:, ::1] c_contig = ...
cdef int[::1, :] f_contig = c_contig.T
This gives a new, transposed, view on the data.
Specifying data layout
======================
Data layout can be specified using the previously seen `::1` slice syntax, or by using any
of the constants in `cython.view`.
The concepts are as follows: there is data access and data packing. Data access means either
direct (no pointer) or indirect (pointer). Generic means you don't know, and want the compiler
Data packing means your data may be strided (e.g. after slicing it, a[::2]) or contiguous
(consecutive elements are adjacent in memory). If no specifier is given in any dimension,
the data access is assumed to be direct, and the data packing assumed to be strided.
If you don't know whether a dimension will be direct or indirect (because you got an object
with a buffer interface from some library perhaps), then you can specify the `generic` flag,
in which case it will be determined at runtime.
The flags are as follows:
cdef generic = Enum("<strided and direct or indirect>")
cdef strided = Enum("<strided and direct>") # default
cdef indirect = Enum("<strided and indirect>")
# Disable generic_contiguous, as it is a troublemaker
#cdef generic_contiguous = Enum("<contiguous and direct or indirect>")
cdef contiguous = Enum("<contiguous and direct>")
cdef indirect_contiguous = Enum("<contiguous and indirect>")
* generic - strided and direct or indirect
* strided - strided and direct (this is the default)
* indirect - strided and indirect (must not be the last dimension)
* contiguous - contiguous and direct
* indirect_contiguous - the list of pointers is contiguous
They can be used as follows::
from cython cimport view
# direct access in both dimensions, strided in the first dimension, contiguous in the last
cdef int[:, ::view.contiguous] a
# contiguous list of pointers to contiguous lists of ints
cdef int[::view.indirect_contiguous, ::1] b
# direct or indirect in the first dimension, direct in the second dimension
# strided in both dimensions
cdef int[::view.generic, :] c
Only the first, last or the dimension following an indirect dimension may be specified contiguous::
# INVALID
cdef int[::view.contiguous, ::view.indirect, :] a
cdef int[::1, ::view.indirect, :] b
# VALID
cdef int[::view.indirect, ::1, :] a
cdef int[::view.indirect, :, ::1] b
cdef int[::view.indirect_contiguous, ::1, :]
The difference between the `contiguous` flag and the `::1` specifier is that the former specifies
contiguity for only one dimension, whereas the latter specifies contiguity for all following (Fortran) or
preceding (C) dimensions::
cdef int[:, ::1] c_contig = ...
# VALID
cdef int[:, ::view.contiguous] myslice = c_contig[::2]
# INVALID
cdef int[:, ::1] myslice = c_contig[::2]
The former case is valid because the last dimension remains contiguous, but the first dimension
does not "follow" the last one anymore (meaning, it was strided already, but it is not C or Fortran
contiguous any longer), since it was sliced.
Memoryview objects and cython.array
===================================
These typed slices can be converted to Python objects (`cython.memoryview`), and are indexable,
slicable and transposable in the same way that the slices are. They can also be converted back to typed
slices at any time.
Cython Array
============
Whenever a slice is copied (using any of the `copy` or `copy_fortran` methods), you get a new
memoryview slice of a newly created cython.array object. This array can also be used manually,
and will automatically allocate a block of data. It can later be assigned to a C or Fortran
contiguous slice (or a strided slice). It can be used like::
import cython
my_array = cython.array(shape=(10, 2), itemsize=sizeof(int), format="i")
cdef int[:, :] my_slice = my_array
It also takes an optional argument `mode` ('c' or 'fortran') and a boolean `allocate_buffer`, that indicates
whether a buffer should be allocated::
cdef cython.array my_array = cython.array(..., mode="fortran", allocate_buffer=False)
my_array.data = <char *> my_data_pointer
# optionally, define a function that can deallocate the data, otherwise
# cython.array will call free() on it
cdef void my_callback(char *data):
... free data if necessary
my_array.callback_free_data = my_callback
You can also cast pointers to arrays::
cdef cython.array my_array = <int[:10, :2]> my_data_pointer
Again, when the array will go out of scope, it will free the data, unless you register a callback like above.
Of course, you can also immidiately assign a cython.array to a typed memoryview slice.
The arrays are indexable and slicable from Python space just like memoryview objects. If you need to do this
a lot, you're better off creating a memoryview object from your array::
memview = cython.memoryview(my_cython_array, PyBUF_C_CONTIGUOUS)
# OR
cdef int[:, ::1] myslice = my_cython_array
memview = myslice
Base Types
==========
As the base type any type may be used (`object`, a struct, etc). If the type name is
not an identifier, you have to create a typedef for it::
ctypedef MyStruct *MyStruct_p
cdef MyStruct_p[:] myslice
The future
==========
In the future some functionality may be added for convenience, like
1. A numpy-like `.flat` attribute (that allows efficient iteration)
2. A numpy-like `.reshape` method
3. A method `to_numpy` which would convert a memoryview object to a NumPy object
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